Legacy files are known to have problems from time to time, and the most reliable way I know to avoid those problems is to export .inx, when possible, from the original version. The second most reliable is to export .idml from the original version.

There are some scripts that will do a batch conversion to .inx or .idml to help you, if you have a lot of files, and if you think you don't have to thoroughly check every legacy file you open in a new version you are sadly mistaken. If you open a .indd file directly, as soon as you start to edit any text it will reflow to confrom to the new text engine and you may not see the problems on the page where you are working. .inx/.idml forces the entire document to recompose as soon as it opens.